Accurate Detection of SARS-CoV-2 by Next-Generation Sequencing in Low Viral Load Specimens

• Published in: International journal of molecular sciences Vol. 24; no. 4; p. 3478
• Main Authors: Ilié, Marius, Benzaquen, Jonathan, Hofman, Véronique, Long-Mira, Elodie, Lassalle, Sandra, Boutros, Jacques, Bontoux, Christophe, Lespinet-Fabre, Virginie, Bordone, Olivier, Tanga, Virginie, Allegra, Maryline, Salah, Myriam, Fayada, Julien, Leroy, Sylvie, Vassallo, Matteo, Touitou, Irit, Courjon, Johan, Contenti, Julie, Carles, Michel, Marquette, Charles-Hugo, Hofman, Paul
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 01.02.2023; MDPI
• Subjects: Analysis; Copy number; Coronaviruses; COVID-19; Disease transmission; DNA sequencing; Genexus; Genomes; Genomics; Health aspects; High-Throughput Nucleotide Sequencing; Humans; low viral load; Metropolitan areas; Next-generation sequencing; Nucleotide sequencing; Pandemics; Retrospective Studies; SARS-CoV-2; Scientific equipment and supplies industry; Severe acute respiratory syndrome coronavirus 2; Viral infections; Viral Load; Workflow; France; United States; COVID-19; Genexus; SARS-CoV-2; low viral load; next generation sequencing
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms24043478

As new SARS-CoV-2 variants emerge, there is an urgent need to increase the efficiency and availability of viral genome sequencing, notably to detect the lineage in samples with a low viral load. SARS-CoV-2 genome next-generation sequencing (NGS) was performed retrospectively in a single center on 175 positive samples from individuals. An automated workflow used the Ion AmpliSeq SARS-CoV-2 Insight Research Assay on the Genexus Sequencer. All samples were collected in the metropolitan area of the city of Nice (France) over a period of 32 weeks (from 19 July 2021 to 11 February 2022). In total, 76% of cases were identified with a low viral load (Ct ≥ 32, and ≤200 copies/µL). The NGS analysis was successful in 91% of cases, among which 57% of cases harbored the Delta variant, and 34% the Omicron BA.1.1 variant. Only 9% of cases had unreadable sequences. There was no significant difference in the viral load in patients infected with the Omicron variant compared to the Delta variant (Ct values, = 0.0507; copy number, = 0.252). We show that the NGS analysis of the SARS-CoV-2 genome provides reliable detection of the Delta and Omicron SARS-CoV-2 variants in low viral load samples.